How to compile EmbryoGen on IT4I's supercomputers

gistfile1.txt

# plan:
# -----
# 1) get EmbryoGen source code
# 2) set up the environment
#   a) with: module add git, then GCC/10.2.0, CMake, OpenMPI/4.0.5-GCC-10.2.0
#   b) calling a script from EmbryoGen's repo
# 3) download, compile and install locally all necessary libs
# 4) setup & compile EmbryoGen


# ...detailed:
# ------------
# 1) get EmbryoGen source code
git clone [email protected]:xulman/EmbryoGen.git
(or: git clone https://github.com/xulman/EmbryoGen.git  ...if it works better for you)
cd EmbryoGen

# 2) set up the environment
. libs/addModulesAtIT4I   (or . libs/addModulesAtIT4I_salomon)

# 3) download, compile and install locally all necessary libs
cd libs
./prepareEverything.sh
# grab a coffee... and note the last printed hint
cd ..

# 4) setup & compile EmbryoGen
mkdir BUILD
cd BUILD
cmake -D FEATURE_RUNDISTRIBUTED=ON  ..    (or cmake -D FEATURE_USEOpenMP=ON  ..)
cmake -D ZeroMQ_DIR=$PWD/../libs/DEPLOY/lib64/cmake/ZeroMQ \
      -D INC_I3D=$PWD/../libs/DEPLOY/include \
      -D INC_GSL=$PWD/../libs/DEPLOY/include \
      -D INC_CPPZMQ=$PWD/../libs/DEPLOY/include \
      -D INC_DAISwp13=$PWD/../libs/DEPLOY/include \
      -D LIB_DAISwp13=$PWD/../libs/DEPLOY/lib64/libDAIS-wp13.a \
      -D SEARCH_ALL_DEPLIBS=ON \
      -D SEARCH_FOR_STATIC=ON \
      -D CMAKE_LIBRARY_PATH=$PWD/../libs/DEPLOY/lib64    ..


# notes:
# ------
# yes, the 'cmake' indeed needs to be run twice!
- in the first run, the standard installation of openmpi is found
- in the second run, the search paths is reset to where we had prepared 3rd party libs,
  in consequence, the openmpi (and openMP too) will no longer be found
- hopefully, CMake does not re-detect what's already been detected...
- and yes, it is normal that quite some error messages are displayed in the first round

# how to override to different installation of OpenMPI?
- start CMake in GUI: ccmake ..
- hit 'T' (advanced options)
- locate MPIEXEC_EXECUTABLE and adjust it to point on the 'mpiexec' you wish to run
- delete (with 'D') all other MPIEXEC_* and MPI_* options
- hopefully, CMake will re-set everything to match the installation of 'mpiexec' of your choice above
- since one sets the path to openmpi explicitly, this operation can be done anytime later